Additional file 1: Tables S2 and S3 show the highly up-regulated and down-regulated genes in the PHA production phase to Selleck Talazoparib the growth phase (F26/F16), respectively. The highly down-regulated genes, i. e. genes with high induction in the growth phase, included flg cluster (H16_B0258-B0271) and two fli clusters (H16_B0561-B0567

and H16_B2360-B2373) related to flagella assembly, as well as several genes in che operon (H16_B0229-B0245) that are related to chemotaxis (Additional file 1: Table S3). Raberg et al. reported that flagellation was strongly occurred during growth and stagnated during PHA biosynthesis [25]. Similar results were obtained in a previous microarray-based comparison of R. eutropha H16 and a PHA-negative mutant PHB-4 [17]. A recent microarray analysis by Brigham et al. reported that PHB production was regulated by a stringent response,

because most of the upstream regions of the strongly up-regulated genes during nitrogen stress contained the consensus elements for σ54-family promoters [22]. Many of the genes were also highly up-regulated by 20–50 fold during the nitrogen-depleted PHA production phase in the present study, such as H16_A0359, H16_A2801, H16_B0780, H16_B0948, https://www.selleckchem.com/products/MDV3100.html and H16_B1156 (Additional file 1: Table S2). A gene cluster that encodes potential nitrogen-scavenging transporters and enzymes (H16_A1075-A1087) was also up-regulated in F26 by 4–16 fold to F16 (data not shown). The expression ratios were much less than 50-491-fold detected in the microarray analysis [22], but the present RNA-seq analysis supported the expression regulation for these genes by the stringent response. Transcriptome changes related to major metabolic processes and cellular functions Sugar degradation The genome analysis of R. eutropha H16 has identified three important clusters participated in fructose degradation in chromosome 2. The genes in cluster 1 (H16_B1497-B1503), which are frcRACBK, pgi2, and zwf2 were significantly induced in the growth phase (Figure 3), suggesting the important roles in transportation and conversion of extracellular fructose to 6-phosphogluconolactone for growth.

The genes in cluster 2, which are glk, zwf3, pgl, and edd2 (H16_B2564-B2567) have roles in sugar phosphorylation and Entner-Doudoroff (ED) pathway. The expression levels MTMR9 of these genes were low in F16 and F26, and slightly increased in F36. The cluster 3 (H16_B1211-B1213), which consists of a gene of putative 2-amino-2-deoxy-D-gluconate hydrolase and kdgK for glucosaminate degradation, and eda involved in ED pathway, was observed to be induced in the growth phase. Figure 3 Expression levels of genes involved in central metabolisms including PHA metabolism in R. eutropha H16 at growth phase F16, PHA production phase F26, and stationary phase F36 on fructose. The log2-transformed RPKM values are visualized using the rainbow color scale in the figure. Genes with the P value above the threshold (P > 0.05) are underlined.